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The crystal structure of mannonate dehydratase from Streptococcus suis serotype2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TZ9 PDB ENTRY 1TZ9
Crystallization Crystal Properties Matthews coefficient Solvent content 2.59 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.69 α = 90 b = 105.69 β = 90 c = 159.572 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.9 105.409 0.12 11.8 13.85 20728 61.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.9 3 0.37 5.7 14.13
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1TZ9 2.9 44.06 19634 1064 99.77 0.2368 0.23401 0.2294 0.28585 0.2746 RANDOM 41.716
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.1 -1.1 2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.973 r_dihedral_angle_4_deg 20.23 r_dihedral_angle_3_deg 19.869 r_dihedral_angle_1_deg 7.293 r_scangle_it 2.2 r_angle_refined_deg 1.636 r_scbond_it 1.341 r_mcangle_it 1.206 r_mcbond_it 0.675 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.973 r_dihedral_angle_4_deg 20.23 r_dihedral_angle_3_deg 19.869 r_dihedral_angle_1_deg 7.293 r_scangle_it 2.2 r_angle_refined_deg 1.636 r_scbond_it 1.341 r_mcangle_it 1.206 r_mcbond_it 0.675 r_nbtor_refined 0.322 r_symmetry_hbond_refined 0.289 r_nbd_refined 0.247 r_symmetry_vdw_refined 0.238 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.113 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5471 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing